Difference between revisions of "WormBase-Caltech Weekly Calls"

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[[WormBase-Caltech_Weekly_Calls_August_2016|August]]
 
 
== August 4, 2016 ==
 
 
 
=== Parasite Paper Pipeline and Curation Status Tracking ===
 
*~4% of Journal articles (roughly, but not precisely, translates to curatable papers) mention both Caenorhabditis species and parasite species
 
*We discussed last week the options for accurately tracking data type flagging and curation status for these papers
 
*SVM does not flag data at the species level, but we need a way to distinguish curation status based on species or it will be difficult to get accurate numbers for Caltech and Hinxton
 
*One option would be to have separate status tables
 
**Lump Caltech and Hinxton species together or distinguish each species separately?
 
*Other options?
 
 
 
=== Intellectual lineage graph ===
 
* Raymond - are we ready to implement as a widget on person page?
 
* Can toggle to show only direct relationships
 
* Will eventually be able to toggle by relationship type
 
* These will simplify complex graphs
 
 
 
=== SVM for MGI ===
 
* Yuling is tying up loose ends for MGI SVM before he leaves
 
 
 
=== AGR Timeline meeting ===
 
* Timeline still pretty high-level but making progress
 
 
 
=== Complex genotype to phenotype annotation ===
 
* Chris - still planning to work out details over models mailing list
 
* We can go ahead with the creation of phenotype report objects to encapsulate complex genotypes
 
* Another approach to consider is whether or not to create "set" objects that contain sets of, for example, alleles, genes, etc.
 
* We could potentially reuse sets as they come up again in different contexts, or in replicate experiments
 
 
 
=== Teleconference line ===
 
* New AT&T conference call is OK, not great
 
* BlueJeans is too expensive for our purposes
 
 
 
 
 
== August 11, 2016 ==
 
 
 
=== Micropublications ===
 
* Would like to make more prominent on homepage
 
* Expanding micropublications to phenotype
 
** Would we require images, photographs of mutant worms
 
** Can clone phenotype form, but remove requirement for publication; also add funding sources
 
** Would negative data require controls?
 
 
 
 
 
== August 18, 2016 ==
 
 
 
=== Citace local upload August 30 ===
 
 
 
=== Tazendra ===
 
* Raymond installing new network card
 
* Recent network crashes, unclear why
 
* Raymond sent a help desk ticket to IMSS; no response so far
 
* Michael and Ranjana have gotten network errors as well (when trying to deal with automated descriptions)
 
 
 
=== Models updating ===
 
* Wen has GitHub page bookmarked to retrieve latest models.wrm file
 
* Older CVS system had used explicit release ID in name of file; not same now with GitHub
 
* With GitHub, it could be easy to script retrieval of latest models.wrm file
 
 
 
=== Anatomy ontology, from OBO to OWL ===
 
* Major reason to do it: make direct connections to terms in other ontologies
 
* Can take advantage of other anatomy ontologies
 
* Should the WBbt "cell" be synonymous with generic "cell" or be referred to as "C. elegans cell"?
 
* Import versus cross-reference approach to linking ontologies
 
 
 
=== Noctua, LEGO curation ===
 
* Weekly meetings, Monday mornings
 
* Nearly ready to release Noctua for use
 
* Ongoing discussion about use of relations from the relations ontology; maybe need some new terms
 
* Idea is to make Noctua the main GO annotation tool, for simple or complex annotations
 
* People still using legacy GAF file, need to transition to OWL format
 
* Training session at end of month (next week)
 
* GO meeting at USC in November; will dedicate the following week to Noctua/LEGO training workshop (Monday Nov 7th?)
 
* While curating need to consider whether a molecular function regulates a process or is part of a process; requires explicit positioning
 
* Need to deal with annotations to a generic gene product versus a specific gene product (one or all isoforms, for example)
 
* Would want a "enabled by product of" relation for genes
 
* Chris M concerned with having too many relations for curators to know/keep track of
 
* Training material should be available from the Noctua homepage
 
 
 
=== Community Phenotype annotation ===
 
* Still sending out emails, reached stopping point, for now (emailed most authors within last month)
 
* Still getting consistent responses from authors
 
* Working on homepage widget to display top contributors
 
 
 
=== Micropublications ===
 
* Daniela had sent out solicitations for expression data; some people expressed interest, but haven't heard back
 
* We could take the phenotype form and modify for micropublication
 
  
  

Revision as of 17:33, 1 September 2016

Previous Years

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2011 Meetings

2012 Meetings

2013 Meetings

2014 Meetings

2015 Meetings


2016 Meetings

January

February

March

April

May

June

July

August


September 1, 2016

Working group discussions

  • More clear about issues surrounding orthology sets
  • ZFIN has protein curation that may be becoming a bit out of date

Single-cell RNA profiling

  • We've been curating some data, but not clear how to display the data
  • Some data sets, like tiling arrays, might conclude genes that are expressed in a cell/tissue
  • Genes that are detected at convincing levels (present call) in cell/tissue
  • Should we display expression data that we do not (or cannot) update differently from other data
  • Simply: is a gene in a cell/tissue or not; is it enriched in a cell/tissue or not
  • Could capture quantitative assessments; transcripts per million, etc.
  • Should we provide an analysis of raw data to users to perform their own comparative analyses
  • Bob Goldstein's group prepared software tools in their paper; could we make use of them?
  • Big question: how do we handle divergent (expression) data?
  • David (Angeles) working on an expression data analysis pipeline
  • Single-cell RNA-Seq data: should it be merged with expression pattern data? Ideally, yes
  • There's difficulty in reconciling small and large datasets (or different data types)
  • Would we want to apply some type of weighting to each type of evidence for a gene-anatomy association, for example
  • In general for expression, it would be great to consolidate data to directly connect genes to anatomy/life stage